Frames Shown in Movie Editor>Mask Mode does not Match Frames Shown in Compositor
I figured it out, and I figured I'd put it on here in case anyone else is having the same problem.
After tracking, I was putting my movie clip through an undistortion node to remove lens distortion, which was changing the positions of objects near the edges, which was why the tracking marker near the edge was so off. I just put my markers through the undistort as well, and now it works perfectly.